Welcome to the jPREdictor project. The program was developed foremost for the
prediction of cis-regulatory elements. Short sequence fragments, namely transcription
factor binding sites, are known to be enriched and clustered in such elements. These
binding sites are represented as motifs and for the prediction, they must be known.
Using these motifs, it is possible to search them on sequences, to weight them by
applying a positive or negative training set (model or background, respectively) and to
score a sequence. Please refer to the manual on how to use the program for the
prediction of regulatory elements. With version 1.22, two new applications were
incorporated into the jPREdictor: motif discovery via motif evolution and the motif
clustering. Both tasks can only be started via command-line. Please refer to the manual
again to get a brief description on how they function and how they are invoked.

Since 24. Apr 2008 version 1.23 of the jPREdictor is available. Some changes were
made to the program, and the motif discovery via evolution and the motif clustering is
finally official. Please refer to the history section for further explanations on
changes and improvements.